Table 3.
Mass spectrometric (MS) parameters used for the LC-MS3 analysis of TMT-labeled peptides
| Parameter | Value |
|---|---|
| Polarity | Positive |
| Source | ESI |
| Spray Voltage | 1800 V |
| Time between master scans (s) | 3 |
| Full MS | |
| Detector type | Orbitrap |
| Orbitrap Resolution | 120000 |
| Automated gain control target (AGC Target) | 2 × 105 |
| Maximum injection time (ms) | 120 |
| Scan Range (m/z) | 380–1500 |
| dd-MS2 | |
| Detector type | Ion trap |
| Ion trap speed | Rapid |
| Automated gain control target (AGC Target) | 1 × 104 |
| Maximum injection time | 50 ms |
| Scan Range (m/z) | 400–1200 |
| Activation type | Collision induced dissociation (CID) |
| CID energy(%) | 35 |
| Monoisotopic peak determination | Peptide |
| Charge exclusion | Include 2-6 |
| Dynamic precursor exclusion | 30 s |
| dd-MS3 | |
| Detector type | Orbitrap |
| Orbitrap Resolution | 50000 |
| Automated gain control target (AGC Target) | 5 × 104 |
| Maximum injection time (ms) | 86 |
| Scan Range (m/z) | 120–500 |
| Activation type | Higher energy collision induced dissociation (CID) |
| HCD energy (%) | 65 |
| Precursor selection mode | Synchronous precursor selection (SPS) Top 10 |